{"id":"W4414640476","doi":"10.1101/2025.09.29.678898","title":"<i>De novo</i> design of phosphotyrosine peptide binders","year":2025,"lang":"en","type":"preprint","venue":"bioRxiv (Cold Spring Harbor Laboratory)","topic":"Chemical Synthesis and Analysis","field":"Biochemistry, Genetics and Molecular Biology","cited_by":2,"is_retracted":false,"has_abstract":true,"ca_institutions":"Queen's University","funders":"Division of Chemistry; National Institute of Allergy and Infectious Diseases; National Cancer Institute; Spark Therapeutics; Washington Research Foundation; Bill and Melinda Gates Foundation; National Science Foundation; Open Philanthropy Project; Defense Threat Reduction Agency; Defense Advanced Research Projects Agency; Cancer Research UK; Leona M. and Harry B. Helmsley Charitable Trust; Advanced Research Projects Agency; National Institutes of Health","keywords":"Phosphorylation; Epidermal growth factor receptor; Peptide; SH2 domain; Tyrosine phosphorylation; Protein–protein interaction; Plasma protein binding; Binding site; Protein design","routes":{"ca_aff":true,"ca_fund":false,"ca_venue":false,"about_ca":false,"invisible_to_affiliation_only":false},"retraction":null,"screen":null,"direct_labels":[],"prediction":{"model_version":"codex-gemma-dda1882f352a","candidate_categories":["metaepi_narrow"],"consensus_categories":[],"category_scores_codex":[0.0004487309,0.0004271728,0.0005568826,0.00011484,0.00006504772,0.00006190786,0.0005937397,0.000637762,0.00004138426],"category_scores_gemma":[0.0003081723,0.0004515695,0.0003406749,0.0003075877,0.0001389111,0.000003495406,0.0005015733,0.0003140731,0.000005779854],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00008290912,"about_ca_system_score_gemma":0.0006119978,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0000539885,"about_ca_topic_score_gemma":0.000001016677,"domain_scores_codex":[0.9979421,0.0001026535,0.0004878378,0.0008216162,0.0002244259,0.000421301],"domain_scores_gemma":[0.9980359,0.00004267745,0.0003298767,0.001114595,0.0003069738,0.000169978],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"bench_or_experimental","study_design_scores_codex":[0.00005937626,0.0001382659,0.001868327,0.0002151321,0.0003403525,0.000005631696,0.000001586573,0.0006145329,0.9954727,0.00004862166,0.001232251,0.000003268798],"study_design_scores_gemma":[0.0002817521,0.0000371498,0.001220762,0.0002298838,0.0002288147,7.978012e-9,0.000001639873,0.0002838534,0.9909745,0.000001852845,0.006293927,0.0004458907],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9504117,0.004455196,0.04345769,0.0002192372,0.0003246265,0.000501412,0.0004702104,0.0000906338,0.00006923119],"genre_scores_gemma":[0.9891466,0.001015637,0.009134724,0.0002890016,0.0002207026,0.0000759942,0.000001545827,0.00005538941,0.00006043115],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.03873481,"threshold_uncertainty_score":0.9997936,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.0103421274111351,"score_gpt":0.2135642149392082,"score_spread":0.2032220875280731,"validation_status":"score_only:v0-immature-baseline","note":"Baseline scores from an immature model (maturity gate not passed). Scores rank; they never assert a category."}}